link

data.matrix <- matrix(nrow=100, ncol=10)
colnames(data.matrix) <- c(
    paste("wt", 1:5, sep=""),
    paste("ko", 1:5, sep=""))
rownames(data.matrix) <- paste("gene", 1:100, sep="")
for (i in 1:100) {
    wt.values <- rpois(5, lambda=sample(x=10:1000, size=1))
    ko.values <- rpois(5, lambda=sample(x=10:1000, size=1))
    
    data.matrix[i,] <- c(wt.values, ko.values)
}
tdata <- t(data.matrix)
head(tdata)
##     gene1 gene2 gene3 gene4 gene5 gene6 gene7 gene8 gene9 gene10 gene11
## wt1   682    14   448   674   325   379    31    24   214    829     11
## wt2   706     8   469   661   316   379    32    29   243    842     10
## wt3   671    13   500   680   367   368    36    26   234    883      8
## wt4   662    15   443   664   367   366    31    21   204    817     12
## wt5   690    10   442   649   343   363    41    25   209    876     11
## ko1   444   164   222   990   736   290   656   538   198    602    848
##     gene12 gene13 gene14 gene15 gene16 gene17 gene18 gene19 gene20 gene21
## wt1    899    252    657    502    863     33    335    581    770     60
## wt2    900    250    677    440    858     39    304    587    748     40
## wt3    919    263    711    449    885     39    310    574    731     56
## wt4    909    239    678    463    860     39    336    554    754     55
## wt5    959    261    690    446    926     34    331    606    747     56
## ko1    548    283    832    922    816    443    498    248    411    694
##     gene22 gene23 gene24 gene25 gene26 gene27 gene28 gene29 gene30 gene31
## wt1    239    689    772    902    357    721     23    562    567     83
## wt2    240    682    860    927    418    726     41    566    599     61
## wt3    234    662    828    844    363    703     29    575    589     82
## wt4    256    668    868    894    379    737     42    579    538     74
## wt5    221    668    792    874    430    682     44    557    559     78
## ko1    351    482    900    743    457    815     75   1013     79    711
##     gene32 gene33 gene34 gene35 gene36 gene37 gene38 gene39 gene40 gene41
## wt1    427    270    367    821    531    691    438    615    444    791
## wt2    438    272    369    785    500    703    458    567    407    852
## wt3    435    285    371    796    565    671    398    605    411    763
## wt4    477    270    355    812    534    704    454    615    408    782
## wt5    401    248    359    797    548    667    426    674    438    812
## ko1    477    747    349    434    486    595    557    132     82    710
##     gene42 gene43 gene44 gene45 gene46 gene47 gene48 gene49 gene50 gene51
## wt1    750    639    348    915    309    680    259    770    352    489
## wt2    748    655    351    914    337    620    297    685    386    464
## wt3    757    652    374    909    311    672    284    765    368    493
## wt4    759    668    368    916    321    633    309    769    390    501
## wt5    771    647    309    930    337    698    274    759    355    478
## ko1    654    550    833    831    890    450    781    297    546    665
##     gene52 gene53 gene54 gene55 gene56 gene57 gene58 gene59 gene60 gene61
## wt1    598    311    258    192    727    337    122    110    637    809
## wt2    594    296    287    203    722    337    103    103    688    840
## wt3    532    307    266    187    689    363    100    116    698    815
## wt4    579    320    283    194    679    330     81    120    711    852
## wt5    532    335    269    199    722    328    101    123    696    767
## ko1    736    603    730    786    209    240    842   1021    836    634
##     gene62 gene63 gene64 gene65 gene66 gene67 gene68 gene69 gene70 gene71
## wt1    616    366    365    813    784    522    672    347    872    185
## wt2    621    319    333    860    805    546    769    390    836    147
## wt3    641    331    322    799    793    508    726    385    835    170
## wt4    644    310    361    822    811    538    707    357    843    189
## wt5    637    333    326    788    813    507    739    372    789    163
## ko1    496    984   1066    888     17    259    781    168    521    897
##     gene72 gene73 gene74 gene75 gene76 gene77 gene78 gene79 gene80 gene81
## wt1    538    954    469    587     67    101    763    749    910    613
## wt2    549    867    470    563     74    125    828    778    942    612
## wt3    489    895    498    621     60     94    735    687   1001    587
## wt4    482    952    446    619     66    118    776    742    928    573
## wt5    537    878    438    606     55    107    757    657    959    581
## ko1    523    345    747    649     77    944    693     15     51    526
##     gene82 gene83 gene84 gene85 gene86 gene87 gene88 gene89 gene90 gene91
## wt1    128    136    367    260    368    444    774    519    288    297
## wt2    108    102    360    297    345    404    845    467    275    291
## wt3     99    110    380    256    380    387    812    521    263    264
## wt4    118    119    366    230    375    433    790    530    260    258
## wt5    149    107    366    250    339    434    773    494    268    283
## ko1    271    830    249    453    136     18    796    163    220    633
##     gene92 gene93 gene94 gene95 gene96 gene97 gene98 gene99 gene100
## wt1    582     92    442    923    967    696    369    780     423
## wt2    563     80    442    904    977    694    357    771     433
## wt3    573     88    437    924    923    686    378    796     408
## wt4    578     70    409    899    988    720    397    766     426
## wt5    517     89    466    913   1006    778    394    749     430
## ko1    390    161    701    672    123    737    816    702     222
head(data.matrix)
##       wt1 wt2 wt3 wt4 wt5 ko1 ko2 ko3 ko4 ko5
## gene1 682 706 671 662 690 444 418 447 464 410
## gene2  14   8  13  15  10 164 179 153 141 159
## gene3 448 469 500 443 442 222 218 251 232 237
## gene4 674 661 680 664 649 990 904 919 884 903
## gene5 325 316 367 367 343 736 702 709 726 696
## gene6 379 379 368 366 363 290 314 296 276 290
pca <- prcomp(t(data.matrix), scale=TRUE) 
summary(pca)
## Importance of components:
##                           PC1     PC2     PC3    PC4     PC5     PC6
## Standard deviation     9.3818 1.77024 1.42646 1.3306 1.23248 1.07882
## Proportion of Variance 0.8802 0.03134 0.02035 0.0177 0.01519 0.01164
## Cumulative Proportion  0.8802 0.91152 0.93187 0.9496 0.96476 0.97640
##                            PC7     PC8     PC9      PC10
## Standard deviation     0.96092 0.89955 0.79205 3.687e-15
## Proportion of Variance 0.00923 0.00809 0.00627 0.000e+00
## Cumulative Proportion  0.98563 0.99373 1.00000 1.000e+00
pca$rotation
##                 PC1           PC2           PC3           PC4
## gene1   -0.10556159 -0.0421504030 -0.0557228266  0.0259194177
## gene2    0.10573872  0.0207481068  0.0013904952 -0.0169430817
## gene3   -0.10544606 -0.0244274884  0.0257177663  0.0078329602
## gene4    0.10431172  0.0025312632  0.0112621854  0.0506631400
## gene5    0.10610598  0.0101549324  0.0166804357  0.0626512834
## gene6   -0.10356908 -0.0160354466 -0.0187685781 -0.0852604890
## gene7    0.10626136 -0.0108835377 -0.0011838748  0.0239803742
## gene8    0.10637336 -0.0031869489 -0.0142360035  0.0053183405
## gene9    0.01508732 -0.2587194411 -0.0458340905 -0.3188903215
## gene10  -0.10486604  0.0036433007 -0.0291485482  0.0520384413
## gene11   0.10650050  0.0016109374 -0.0021037596  0.0059457294
## gene12  -0.10560365  0.0251082675  0.0004119449 -0.0013953103
## gene13   0.09113077 -0.0517730356 -0.1617072893  0.2516914659
## gene14   0.10393936 -0.0052875190  0.0104146802  0.0813333385
## gene15   0.10592585  0.0065475880 -0.0017959566  0.0428845707
## gene16  -0.05975260  0.3440133704 -0.1945658138 -0.2050250073
## gene17   0.10635107 -0.0049608455 -0.0001535922  0.0044717932
## gene18   0.10410131  0.0223988571 -0.0146929166  0.1064774666
## gene19  -0.10627027  0.0052176933 -0.0321130670 -0.0144658096
## gene20  -0.10632085 -0.0006435921  0.0070163084 -0.0047984011
## gene21   0.10611896 -0.0029379504 -0.0273266196  0.0496980808
## gene22   0.10116047 -0.0541292100 -0.0343035086  0.0998260227
## gene23  -0.10541809  0.0057701360  0.0154188730 -0.0546182693
## gene24   0.09063823 -0.1397095836  0.1326768833 -0.0989659786
## gene25  -0.09844459 -0.1049456790 -0.0724162196 -0.1020150304
## gene26   0.08499020  0.0766355968 -0.1612621674 -0.3196776116
## gene27   0.09874203 -0.0524613586  0.1777039580 -0.1523357655
## gene28   0.09975550  0.0436701795 -0.0269037121 -0.1637253164
## gene29   0.10629415 -0.0044468119 -0.0024224063  0.0327332346
## gene30  -0.10631525 -0.0239487514  0.0006777606 -0.0161973084
## gene31   0.10639858 -0.0002530170 -0.0115059351  0.0310466736
## gene32   0.08432073 -0.1062223327  0.3550494939 -0.0705410470
## gene33   0.10599640 -0.0025909629 -0.0040088332  0.0041751665
## gene34  -0.09372548 -0.0820813958 -0.0213992367  0.0600918142
## gene35  -0.10628242  0.0055874146  0.0295752127  0.0093036792
## gene36  -0.08802190  0.1779263094  0.0396391874  0.1703590469
## gene37  -0.08916559 -0.0535619170  0.0038239523 -0.1363705285
## gene38   0.10258829 -0.0380620550 -0.0137076564 -0.0953799014
## gene39  -0.10595666  0.0502442334 -0.0071701258  0.0005750266
## gene40  -0.10630817  0.0192980982 -0.0013250382 -0.0103907175
## gene41  -0.09508663 -0.1289745507 -0.2121459775 -0.1327372313
## gene42  -0.10002403  0.0437595747 -0.0981679991  0.0478537316
## gene43  -0.10340193 -0.0059301801  0.0157670289 -0.0338569127
## gene44   0.10603196 -0.0186336810  0.0228297599  0.0231104820
## gene45  -0.09757410  0.0019357100  0.0499354906  0.0129553276
## gene46   0.10623968 -0.0004895773 -0.0322379065 -0.0047268320
## gene47  -0.10197771  0.1021893528  0.0137435929 -0.0374630904
## gene48   0.10624879 -0.0209998358 -0.0013450778  0.0272261427
## gene49  -0.10594131  0.0314745987  0.0239523847  0.0516413311
## gene50   0.10467547 -0.0369460107  0.0775154372 -0.0655472857
## gene51   0.10464052  0.0349929437  0.0108735647  0.0723103045
## gene52   0.10227552 -0.0911144963  0.0158329217  0.0107012259
## gene53   0.10572090  0.0577463406  0.0083008919 -0.0325758004
## gene54   0.10631276 -0.0110889009  0.0061180569  0.0011170545
## gene55   0.10621612 -0.0122192395 -0.0341797820  0.0369901704
## gene56  -0.10640086 -0.0049122389 -0.0256650599 -0.0195200651
## gene57  -0.10417734 -0.0466573025  0.0446155593  0.0589969279
## gene58   0.10637836  0.0006953797 -0.0182324967  0.0115806056
## gene59   0.10639660  0.0132621798 -0.0102287745  0.0099314227
## gene60   0.10140712  0.0440620754  0.0380560078 -0.0243083931
## gene61  -0.09836676 -0.1497580428  0.0544200824  0.0893231445
## gene62  -0.10486284  0.0011856468  0.0317829874  0.0545252043
## gene63   0.10630409  0.0112337984 -0.0076481154  0.0076213140
## gene64   0.10622580 -0.0013679530  0.0171124448 -0.0027957631
## gene65   0.07680151 -0.2256937569  0.0623863580 -0.2510135717
## gene66  -0.10644399  0.0029012703  0.0069527275 -0.0176645640
## gene67  -0.10585202 -0.0199876504  0.0287597806 -0.0612677980
## gene68   0.07510557 -0.1612819903 -0.3002698323 -0.0451651980
## gene69  -0.10542128 -0.0173354764  0.0009685020 -0.0567048396
## gene70  -0.10519254 -0.0293793344  0.0648875286 -0.0094629600
## gene71   0.10634360  0.0032162186  0.0017749006  0.0376466985
## gene72   0.01882213 -0.2077581267 -0.5683212645  0.0235589238
## gene73  -0.10609094  0.0097381219  0.0480685826  0.0122987546
## gene74   0.10574230 -0.0294536469  0.0203654108  0.0300279209
## gene75   0.08444863  0.1923059709  0.2534510686 -0.1004997325
## gene76   0.07929629 -0.1445791751  0.2077836421 -0.3526721913
## gene77   0.10646477 -0.0137462869 -0.0153382492  0.0247675981
## gene78  -0.09524695 -0.1274246353 -0.0738205336 -0.1243738844
## gene79  -0.10606921 -0.0366628008  0.0246777830 -0.0320558016
## gene80  -0.10638588  0.0054450397  0.0105623360 -0.0104717788
## gene81  -0.08600602 -0.0643393248  0.0248887948 -0.3263069601
## gene82   0.10351919  0.0710293052 -0.0918919172  0.0039416549
## gene83   0.10636071 -0.0076130352 -0.0037665287  0.0271382056
## gene84  -0.10287625  0.0499084604 -0.0122489575  0.0209218278
## gene85   0.10173729 -0.0450186622 -0.0716280898 -0.0702813334
## gene86  -0.10557624  0.0093665077  0.0396143690  0.0329433427
## gene87  -0.10620296  0.0176644227  0.0067478501 -0.0131328562
## gene88  -0.03605430 -0.4646573771 -0.0634233052  0.0916291580
## gene89  -0.10604115  0.0255607792  0.0530675297  0.0230311236
## gene90  -0.10234180  0.0022991417 -0.0314755440 -0.0421367449
## gene91   0.10568679  0.0083368128 -0.0424684715 -0.0227203139
## gene92  -0.10353843 -0.0611567955  0.1135344554  0.0473995629
## gene93   0.10292872  0.0173536250 -0.0062411610 -0.0264710050
## gene94   0.10511157  0.0144473382 -0.0845885395  0.0047199636
## gene95  -0.10572842  0.0246675543 -0.0066649858 -0.0120002776
## gene96  -0.10632064  0.0091854009 -0.0033428331 -0.0215180851
## gene97   0.02623869  0.4364446726 -0.2216418371 -0.2819894364
## gene98   0.10607019  0.0210911626 -0.0159949738  0.0410304662
## gene99  -0.09663728 -0.0893190502  0.0594852359  0.0877502870
## gene100 -0.10563872 -0.0271600266 -0.0255112099 -0.0068283767
##                   PC5          PC6           PC7           PC8
## gene1    0.0509811188 -0.008697572 -0.0325659585  0.0158875714
## gene2   -0.0403348743  0.014440407  0.0635618629 -0.0667496002
## gene3   -0.0312309137 -0.062744576 -0.0597038679  0.0806717073
## gene4    0.0728057181  0.013306191  0.0064283865 -0.0493156906
## gene5    0.0027321381 -0.030847036  0.0056850792 -0.0066830321
## gene6   -0.0641365984  0.047986328  0.1305120304 -0.0699231204
## gene7   -0.0085379103  0.012371740 -0.0523527347  0.0052093286
## gene8   -0.0427473323  0.015442618  0.0084957745  0.0216055746
## gene9   -0.5911797326 -0.137737246 -0.1573281973  0.1114750204
## gene10   0.0395786436 -0.084748048 -0.0948016371 -0.0826921624
## gene11   0.0039031576  0.011938988 -0.0079286074 -0.0309419227
## gene12   0.0602341323 -0.045704682 -0.0795843419 -0.0396337072
## gene13  -0.1512334203 -0.046305346 -0.2030576134  0.0153229192
## gene14   0.0050521984 -0.123900176 -0.1422654469  0.0219073819
## gene15   0.0129145678  0.073223108  0.0193287389  0.0128668257
## gene16  -0.2556006801 -0.153498790 -0.0662700058  0.2004539269
## gene17  -0.0324252750  0.014129517 -0.0166565856  0.0451997618
## gene18   0.0718885155  0.067866858  0.0096127502  0.1060669440
## gene19   0.0243102872 -0.012187717 -0.0421807629 -0.0275515251
## gene20   0.0323423387  0.034114677  0.0052174212  0.0371313109
## gene21  -0.0264438188  0.017415195  0.0340883169  0.0217997601
## gene22  -0.0827252980  0.008937201  0.2525987195 -0.0196237772
## gene23   0.0569570316  0.052454389 -0.0253180179  0.0811118441
## gene24   0.0611046934 -0.291665445  0.1838718931  0.1690382406
## gene25  -0.0285460852  0.084753806  0.2187084855 -0.1511219272
## gene26   0.1781734141 -0.150151427 -0.1627347564  0.1196726052
## gene27   0.0572964293  0.076704730  0.0509262272 -0.1198462317
## gene28   0.1227647218 -0.171419951  0.0404958513 -0.0988761226
## gene29   0.0101664770 -0.002819164  0.0291053823 -0.0215421922
## gene30   0.0073815440 -0.022978666 -0.0444721449 -0.0164776854
## gene31  -0.0217371796  0.015524351  0.0056509399 -0.0260361795
## gene32   0.0509682076 -0.038687735  0.0375014448  0.0991801381
## gene33  -0.0424091175  0.005198625  0.0535545177 -0.0396545487
## gene34   0.0737093379  0.029236357 -0.2018651692  0.1859067785
## gene35   0.0392666816  0.018216150 -0.0187569731  0.0008405101
## gene36  -0.2075729016 -0.166345966  0.0336561997 -0.2667751562
## gene37  -0.1197423969  0.081592246  0.4182677092  0.2880772564
## gene38   0.1213471771  0.080660682  0.1546788281  0.0264644409
## gene39   0.0237310441 -0.013215351 -0.0245668527 -0.0091984411
## gene40   0.0212247460  0.027634501 -0.0346442742 -0.0330071216
## gene41   0.0791658512 -0.016897033  0.0758599981 -0.1054020720
## gene42  -0.1550451444 -0.069632224  0.1870135748  0.0286866871
## gene43  -0.0315692772 -0.103453105  0.1951690379 -0.0938269103
## gene44  -0.0448644021  0.012139390  0.0069247606  0.0704963420
## gene45   0.2152646502 -0.007136010 -0.2791262833  0.0065709868
## gene46  -0.0413045118  0.001060162  0.0418438651 -0.0150653625
## gene47  -0.0703677198  0.049966518 -0.1872042444  0.0133232693
## gene48  -0.0091451901 -0.012100562  0.0063411635  0.0468029743
## gene49  -0.0148611161  0.002301887  0.0224433787 -0.0226683722
## gene50   0.0356679619 -0.044132314 -0.0531653446 -0.0548919213
## gene51  -0.0137380001  0.019762769  0.1034103389  0.0910427463
## gene52   0.0054839769  0.145651260  0.0033727891  0.1242228373
## gene53   0.0279483761  0.012811421 -0.0192612812  0.0035218034
## gene54   0.0426401632 -0.008017560 -0.0229158741 -0.0355831390
## gene55  -0.0181998718  0.009284150  0.0346486991 -0.0034034529
## gene56   0.0040663969  0.012166102 -0.0004104864 -0.0379947583
## gene57  -0.0887030985 -0.067337381 -0.0874279711 -0.0645587543
## gene58  -0.0159920938  0.029134030  0.0052834529 -0.0179344773
## gene59  -0.0046060192  0.012412878  0.0138874456  0.0343649989
## gene60   0.1012129608 -0.190942958 -0.0030120341  0.1732006915
## gene61  -0.0335470648 -0.036591924  0.1554168421  0.0752855050
## gene62   0.0476984712 -0.098354327 -0.0232260262 -0.0752749977
## gene63  -0.0101434302  0.047266584 -0.0179090838  0.0047362666
## gene64   0.0045814430  0.033195507 -0.0035302284 -0.0774025655
## gene65   0.0616574223 -0.005295725  0.0816990540 -0.4830370086
## gene66   0.0235276572 -0.026418533  0.0018970677 -0.0114070490
## gene67   0.0447450336 -0.007797256  0.0326255145 -0.0102639652
## gene68   0.0455330264 -0.440561215  0.0521469848 -0.0073399536
## gene69   0.0049658115 -0.091256448 -0.0491706478 -0.0534105745
## gene70   0.0359062847  0.041252592 -0.0121210967 -0.1114516760
## gene71   0.0035316017  0.027303853  0.0005804455  0.0376932152
## gene72   0.0081923911  0.341810182 -0.0889426711 -0.0635846558
## gene73   0.0322171237  0.033549691  0.0301670688 -0.0128177117
## gene74  -0.0400130184  0.006916136 -0.0591805964 -0.0064633768
## gene75  -0.1468051350 -0.134233779 -0.1127161292 -0.2079875679
## gene76   0.0631219433  0.169346142 -0.1613855513  0.1083148155
## gene77   0.0043066809  0.008943114  0.0046143095 -0.0040907504
## gene78   0.2334207846 -0.002373430  0.1209652601  0.0939640998
## gene79   0.0312873504  0.017309693  0.0245196192 -0.0073399182
## gene80  -0.0013228671 -0.048207807 -0.0246634484 -0.0031484490
## gene81  -0.1855554888  0.246266558 -0.1395228577  0.0035473259
## gene82   0.0163838837  0.050716357  0.0863837803 -0.1274485999
## gene83  -0.0249991111  0.030668120 -0.0022994533 -0.0190025507
## gene84   0.0045200673 -0.026691950  0.1006835176  0.1535852117
## gene85   0.0349289983  0.012628893  0.0135149973 -0.1031924880
## gene86  -0.0052517386 -0.014728424  0.0881305297  0.0000486805
## gene87   0.0389263467  0.031026263  0.0133161856 -0.0230360301
## gene88   0.1214548297 -0.350930771 -0.1359516499 -0.0148361984
## gene89   0.0210725957 -0.003500205  0.0194660270 -0.0218104403
## gene90   0.0951658488  0.154273335 -0.0159408251 -0.0334513021
## gene91  -0.0480108575  0.053744762  0.0403248128  0.0414676697
## gene92   0.0738990243  0.042835068 -0.0563440357  0.0374163726
## gene93  -0.0694542950  0.060819965 -0.1576110060 -0.1944970444
## gene94  -0.0720689498  0.014576931  0.0288011666 -0.0550922203
## gene95  -0.0575221340  0.016412267  0.0146356738  0.0945634791
## gene96   0.0457112312 -0.009451364  0.0070434462 -0.0006282281
## gene97   0.2004768030 -0.133372903  0.0851956456 -0.1095302769
## gene98   0.0002465353  0.002377243  0.0318507560  0.0688457150
## gene99  -0.2229793055 -0.019963704  0.0912813342 -0.2132883093
## gene100  0.0040627529 -0.009838983  0.0242601151 -0.0612751442
##                  PC9          PC10
## gene1   -0.037796166 -0.2225145869
## gene2    0.079705703 -0.0306452709
## gene3    0.073522725 -0.1044842108
## gene4    0.208198209  0.1048768796
## gene5    0.006339721 -0.0374330820
## gene6    0.143187322 -0.2505626224
## gene7   -0.055183941 -0.0126246167
## gene8   -0.009445943  0.0321289283
## gene9    0.004934811 -0.0592237902
## gene10   0.038671249 -0.0503918069
## gene11   0.029993377 -0.0164591758
## gene12  -0.046695489 -0.0489580618
## gene13  -0.177481759  0.0263008667
## gene14  -0.012766811 -0.0924654104
## gene15   0.057037673 -0.0710981287
## gene16   0.017592744  0.1556157890
## gene17  -0.031283980  0.0155997278
## gene18  -0.051371102  0.0040954087
## gene19  -0.012346876  0.0330823735
## gene20  -0.035813326 -0.0662893316
## gene21   0.004722280  0.0078069500
## gene22  -0.023104529  0.1338396276
## gene23   0.055613401  0.0870585272
## gene24  -0.075320263  0.3069645740
## gene25  -0.133195944 -0.1297146898
## gene26  -0.048277087 -0.0351491513
## gene27   0.056543160  0.0045489492
## gene28  -0.065487802  0.0970880502
## gene29   0.059698818 -0.0403790830
## gene30   0.014383667 -0.0424312251
## gene31   0.006091929 -0.0245941840
## gene32  -0.305556516  0.0721188307
## gene33   0.083035343 -0.0289460779
## gene34   0.443741657  0.2462763104
## gene35  -0.032571136  0.0171296674
## gene36   0.112719830  0.0371632486
## gene37   0.008252431 -0.0237932496
## gene38   0.007708502  0.0551966457
## gene39  -0.058334805  0.0121304844
## gene40  -0.023402791  0.0282761445
## gene41  -0.090434824  0.0994832534
## gene42  -0.152616158 -0.2286811557
## gene43   0.001412422 -0.0751516011
## gene44  -0.008149236  0.0189280752
## gene45  -0.150434514 -0.0534254188
## gene46   0.001482313 -0.0396984371
## gene47  -0.098879589  0.0741026111
## gene48  -0.050092898  0.0385241714
## gene49  -0.055120775  0.0386831850
## gene50  -0.059624197 -0.0536765905
## gene51   0.094263778  0.1225522521
## gene52  -0.156383303 -0.0821829098
## gene53   0.056873458  0.0263624385
## gene54   0.024372121  0.0097212145
## gene55   0.001518812  0.0063105986
## gene56  -0.011058961  0.0042173934
## gene57   0.009027199 -0.1393892728
## gene58   0.046844227 -0.0224865836
## gene59   0.046022379  0.0149491144
## gene60   0.063363284  0.0009830317
## gene61  -0.210289007  0.1512254468
## gene62  -0.089375567  0.0689555815
## gene63   0.051386638 -0.0399688181
## gene64   0.005612978 -0.0252429499
## gene65   0.039004475  0.0149751042
## gene66  -0.021354449  0.0101321957
## gene67   0.006392322  0.0226071244
## gene68   0.072671714 -0.2626490105
## gene69   0.037654821  0.0287197519
## gene70   0.027663262  0.0064042791
## gene71   0.005726213  0.0195374247
## gene72  -0.213892599  0.1908295625
## gene73  -0.017988102  0.0071672379
## gene74   0.088518431 -0.0965238803
## gene75  -0.108346816  0.1085833303
## gene76  -0.005364649 -0.2320819463
## gene77  -0.006214708 -0.0290336754
## gene78   0.117870040  0.0435864293
## gene79  -0.006921544 -0.0028341557
## gene80   0.005972088 -0.0120686739
## gene81   0.092018403  0.2579299436
## gene82   0.022645062  0.0128766680
## gene83  -0.026165177  0.0029621835
## gene84   0.219636146 -0.0677282232
## gene85   0.289587521 -0.0747127828
## gene86   0.098308900  0.0010588056
## gene87  -0.054234014  0.0206001066
## gene88   0.068571997  0.1523992290
## gene89   0.013752093 -0.0191263834
## gene90   0.219907262 -0.0471076079
## gene91   0.060618643 -0.0527124893
## gene92   0.002598054  0.0266747948
## gene93   0.009917979 -0.0533803975
## gene94   0.038374892 -0.0151866742
## gene95   0.041159134 -0.1432165062
## gene96  -0.031026621 -0.0134034581
## gene97  -0.075387360  0.1334570665
## gene98   0.008289848  0.0540232888
## gene99   0.136512725  0.3026739712
## gene100 -0.128254514  0.0173264974
pca$x
##           PC1          PC2         PC3         PC4        PC5          PC6
## wt1 -9.370823  0.079904160  0.24497886  0.54653184 -0.2975869  2.777986577
## wt2 -8.741505 -3.622653102 -1.24528906 -1.80750487  0.4852468 -0.394818993
## wt3 -9.090201 -0.011179552  1.22421644  1.31699663 -1.5933882 -1.339842142
## wt4 -8.430157  0.511531009  2.27687400  0.05905742  1.0831721 -0.549020895
## wt5 -8.839979  3.048001224 -2.40790089 -0.21331091  0.4502512 -0.574948837
## ko1  9.230789  0.002167775  0.03072004  0.82944925  2.3341824 -0.218583571
## ko2  8.693171  0.227411076 -0.59608274 -0.75460902 -1.9731572 -0.152755368
## ko3  8.422925  0.503297082 -1.03306982  0.77878294 -0.1341067  0.183484188
## ko4  8.842555 -1.941512862 -0.15953149  1.67602419 -0.2465121  0.004485865
## ko5  9.283223  1.203033190  1.66508465 -2.43141746 -0.1081015  0.264013175
##             PC7         PC8         PC9         PC10
## wt1 -0.13211666 -0.27628392  0.25030462 1.481454e-15
## wt2  0.01455959  0.23430161  0.22339914 2.137179e-15
## wt3 -0.91801987  0.08373687  0.90644455 2.081668e-15
## wt4  1.54933894  0.11978434 -0.79622660 3.004541e-15
## wt5 -0.52869060 -0.19740582 -0.61560816 3.459039e-15
## ko1 -0.22212116 -1.04129878  1.03923996 4.066192e-15
## ko2  1.33659274 -1.33299623  0.09671415 3.620368e-15
## ko3  0.91153448  1.99859512  0.54252279 3.594347e-15
## ko4 -0.80428094 -0.06888289 -1.51594111 3.086073e-15
## ko5 -1.20679652  0.48044969 -0.13084934 4.291706e-15
library(ggbiplot)
## Loading required package: ggplot2
## Loading required package: plyr
## Loading required package: scales
## Loading required package: grid
ggbiplot(pca)

ggbiplot(pca, labels=rownames(tdata))

## plot pc1 and pc2
plot(pca$x[,1], pca$x[,2])

## make a scree plot
pca.var <- pca$sdev^2
pca.var.per <- round(pca.var/sum(pca.var)*100, 1)
barplot(pca.var.per, main="Scree Plot", xlab="Principal Component", ylab="Percent Variation")

library(ggplot2)

pca.data <- data.frame(Sample=rownames(pca$x),
                       X=pca$x[,1],
                       Y=pca$x[,2])
pca.data
##     Sample         X            Y
## wt1    wt1 -9.370823  0.079904160
## wt2    wt2 -8.741505 -3.622653102
## wt3    wt3 -9.090201 -0.011179552
## wt4    wt4 -8.430157  0.511531009
## wt5    wt5 -8.839979  3.048001224
## ko1    ko1  9.230789  0.002167775
## ko2    ko2  8.693171  0.227411076
## ko3    ko3  8.422925  0.503297082
## ko4    ko4  8.842555 -1.941512862
## ko5    ko5  9.283223  1.203033190
ggplot(data=pca.data, aes(x=X, y=Y, label=Sample)) +
    geom_text() +
    xlab(paste("PC1 - ", pca.var.per[1], "%", sep="")) +
    ylab(paste("PC2 - ", pca.var.per[2], "%", sep="")) +
    theme_bw() +
    ggtitle("My PCA Graph")

loading_scores <- pca$rotation[,1]

loading_scores
##       gene1       gene2       gene3       gene4       gene5       gene6 
## -0.10556159  0.10573872 -0.10544606  0.10431172  0.10610598 -0.10356908 
##       gene7       gene8       gene9      gene10      gene11      gene12 
##  0.10626136  0.10637336  0.01508732 -0.10486604  0.10650050 -0.10560365 
##      gene13      gene14      gene15      gene16      gene17      gene18 
##  0.09113077  0.10393936  0.10592585 -0.05975260  0.10635107  0.10410131 
##      gene19      gene20      gene21      gene22      gene23      gene24 
## -0.10627027 -0.10632085  0.10611896  0.10116047 -0.10541809  0.09063823 
##      gene25      gene26      gene27      gene28      gene29      gene30 
## -0.09844459  0.08499020  0.09874203  0.09975550  0.10629415 -0.10631525 
##      gene31      gene32      gene33      gene34      gene35      gene36 
##  0.10639858  0.08432073  0.10599640 -0.09372548 -0.10628242 -0.08802190 
##      gene37      gene38      gene39      gene40      gene41      gene42 
## -0.08916559  0.10258829 -0.10595666 -0.10630817 -0.09508663 -0.10002403 
##      gene43      gene44      gene45      gene46      gene47      gene48 
## -0.10340193  0.10603196 -0.09757410  0.10623968 -0.10197771  0.10624879 
##      gene49      gene50      gene51      gene52      gene53      gene54 
## -0.10594131  0.10467547  0.10464052  0.10227552  0.10572090  0.10631276 
##      gene55      gene56      gene57      gene58      gene59      gene60 
##  0.10621612 -0.10640086 -0.10417734  0.10637836  0.10639660  0.10140712 
##      gene61      gene62      gene63      gene64      gene65      gene66 
## -0.09836676 -0.10486284  0.10630409  0.10622580  0.07680151 -0.10644399 
##      gene67      gene68      gene69      gene70      gene71      gene72 
## -0.10585202  0.07510557 -0.10542128 -0.10519254  0.10634360  0.01882213 
##      gene73      gene74      gene75      gene76      gene77      gene78 
## -0.10609094  0.10574230  0.08444863  0.07929629  0.10646477 -0.09524695 
##      gene79      gene80      gene81      gene82      gene83      gene84 
## -0.10606921 -0.10638588 -0.08600602  0.10351919  0.10636071 -0.10287625 
##      gene85      gene86      gene87      gene88      gene89      gene90 
##  0.10173729 -0.10557624 -0.10620296 -0.03605430 -0.10604115 -0.10234180 
##      gene91      gene92      gene93      gene94      gene95      gene96 
##  0.10568679 -0.10353843  0.10292872  0.10511157 -0.10572842 -0.10632064 
##      gene97      gene98      gene99     gene100 
##  0.02623869  0.10607019 -0.09663728 -0.10563872
gene_scores <- abs(loading_scores) ## get the magnitudes
gene_score_ranked <- sort(gene_scores, decreasing=TRUE)
top_10_genes <- names(gene_score_ranked[1:10])

top_10_genes ## show the names of the top 10 genes
##  [1] "gene11" "gene77" "gene66" "gene56" "gene31" "gene59" "gene80"
##  [8] "gene58" "gene8"  "gene83"
pca$rotation[top_10_genes,1] ## show the scores (and +/- sign)
##     gene11     gene77     gene66     gene56     gene31     gene59 
##  0.1065005  0.1064648 -0.1064440 -0.1064009  0.1063986  0.1063966 
##     gene80     gene58      gene8     gene83 
## -0.1063859  0.1063784  0.1063734  0.1063607
tdata <- t(data.matrix)
heatmap(tdata)